Multiple sequence alignment - TraesCS6D01G157800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G157800 chr6D 100.000 4079 0 0 1 4079 134338588 134334510 0.000000e+00 7533.0
1 TraesCS6D01G157800 chr6D 97.719 3508 44 6 574 4079 134742931 134739458 0.000000e+00 6002.0
2 TraesCS6D01G157800 chr6D 89.898 1970 161 24 1092 3040 134588309 134586357 0.000000e+00 2501.0
3 TraesCS6D01G157800 chr6D 89.792 1969 165 22 1092 3040 135041759 135039807 0.000000e+00 2490.0
4 TraesCS6D01G157800 chr6D 96.441 590 19 2 1 589 134743713 134743125 0.000000e+00 972.0
5 TraesCS6D01G157800 chr6D 83.333 192 30 1 3865 4056 357725512 357725323 4.190000e-40 176.0
6 TraesCS6D01G157800 chr6D 92.308 78 6 0 1715 1792 33243212 33243135 1.200000e-20 111.0
7 TraesCS6D01G157800 chr6B 95.488 2305 93 4 799 3098 233089210 233086912 0.000000e+00 3670.0
8 TraesCS6D01G157800 chr6B 89.228 1968 178 20 1092 3040 233674004 233672052 0.000000e+00 2429.0
9 TraesCS6D01G157800 chr6B 88.542 288 24 7 3323 3604 693905998 693906282 1.400000e-89 340.0
10 TraesCS6D01G157800 chr6B 87.805 287 33 2 3795 4079 233044617 233044331 6.530000e-88 335.0
11 TraesCS6D01G157800 chr6B 98.913 92 1 0 716 807 233090873 233090782 9.070000e-37 165.0
12 TraesCS6D01G157800 chr6B 92.857 112 6 2 3609 3719 233085684 233085574 1.170000e-35 161.0
13 TraesCS6D01G157800 chr6B 91.935 62 5 0 3137 3198 402237869 402237930 2.020000e-13 87.9
14 TraesCS6D01G157800 chr6B 87.324 71 8 1 3128 3198 37259841 37259910 3.380000e-11 80.5
15 TraesCS6D01G157800 chr6A 95.408 1655 72 3 1482 3135 175997191 175995540 0.000000e+00 2632.0
16 TraesCS6D01G157800 chr6A 89.690 1969 167 22 1092 3040 176293959 176292007 0.000000e+00 2479.0
17 TraesCS6D01G157800 chr6A 94.314 598 25 4 649 1246 176003389 176002801 0.000000e+00 907.0
18 TraesCS6D01G157800 chr6A 96.757 185 6 0 1241 1425 175997372 175997188 3.960000e-80 309.0
19 TraesCS6D01G157800 chr6A 81.754 285 33 7 3795 4079 175992425 175992160 1.910000e-53 220.0
20 TraesCS6D01G157800 chr6A 100.000 28 0 0 3694 3721 175992518 175992491 7.000000e-03 52.8
21 TraesCS6D01G157800 chr3D 94.118 612 35 1 1 611 549233909 549234520 0.000000e+00 929.0
22 TraesCS6D01G157800 chr3D 93.137 612 41 1 1 611 157181942 157182553 0.000000e+00 896.0
23 TraesCS6D01G157800 chr3D 92.997 614 40 3 1 611 511422501 511421888 0.000000e+00 893.0
24 TraesCS6D01G157800 chr3D 82.803 157 26 1 3865 4020 469821062 469821218 5.500000e-29 139.0
25 TraesCS6D01G157800 chr3D 95.238 63 3 0 3137 3199 288297400 288297338 2.590000e-17 100.0
26 TraesCS6D01G157800 chr3D 87.209 86 10 1 3129 3213 591338362 591338447 3.360000e-16 97.1
27 TraesCS6D01G157800 chr3D 93.443 61 4 0 3138 3198 524646283 524646223 1.560000e-14 91.6
28 TraesCS6D01G157800 chr4D 93.821 615 37 1 1 614 360461947 360461333 0.000000e+00 924.0
29 TraesCS6D01G157800 chr2D 93.669 616 37 2 1 615 391827413 391826799 0.000000e+00 920.0
30 TraesCS6D01G157800 chr2D 93.475 613 36 4 1 611 200802199 200802809 0.000000e+00 907.0
31 TraesCS6D01G157800 chr2D 92.581 620 43 3 1 619 203459406 203458789 0.000000e+00 887.0
32 TraesCS6D01G157800 chr2D 74.123 912 196 32 2094 2974 565090943 565091845 1.400000e-89 340.0
33 TraesCS6D01G157800 chr2D 88.421 285 29 3 3323 3604 639489336 639489053 1.400000e-89 340.0
34 TraesCS6D01G157800 chr2D 86.486 296 35 4 3323 3613 611247959 611247664 1.830000e-83 320.0
35 TraesCS6D01G157800 chr2D 86.644 292 31 6 3323 3610 331766734 331767021 2.370000e-82 316.0
36 TraesCS6D01G157800 chr2D 75.794 661 135 19 2094 2732 565052904 565053561 1.100000e-80 311.0
37 TraesCS6D01G157800 chr2D 81.771 192 34 1 3865 4056 480159539 480159729 4.220000e-35 159.0
38 TraesCS6D01G157800 chr7D 92.857 616 43 1 1 615 383276892 383277507 0.000000e+00 893.0
39 TraesCS6D01G157800 chr7D 74.020 612 127 26 1101 1699 30264403 30264995 1.910000e-53 220.0
40 TraesCS6D01G157800 chr7D 89.474 76 8 0 3138 3213 1357007 1357082 3.360000e-16 97.1
41 TraesCS6D01G157800 chr2A 76.444 658 133 14 2094 2732 705532001 705532655 1.820000e-88 337.0
42 TraesCS6D01G157800 chr1D 87.719 285 31 3 3323 3604 287170838 287170555 3.040000e-86 329.0
43 TraesCS6D01G157800 chr7A 86.424 302 34 5 3306 3604 269124989 269125286 1.410000e-84 324.0
44 TraesCS6D01G157800 chr5D 86.644 292 35 3 3323 3610 397331785 397331494 1.830000e-83 320.0
45 TraesCS6D01G157800 chr2B 75.831 662 136 14 2094 2732 676747731 676748391 8.510000e-82 315.0
46 TraesCS6D01G157800 chr2B 78.469 209 45 0 3848 4056 655654720 655654512 1.980000e-28 137.0
47 TraesCS6D01G157800 chr1B 86.760 287 33 4 3322 3604 456275788 456275503 8.510000e-82 315.0
48 TraesCS6D01G157800 chr1B 83.019 106 14 4 3111 3213 675697773 675697877 4.340000e-15 93.5
49 TraesCS6D01G157800 chr4A 74.138 696 137 32 1091 1767 698171061 698170390 8.760000e-62 248.0
50 TraesCS6D01G157800 chr7B 81.988 161 29 0 3865 4025 537986254 537986414 1.980000e-28 137.0
51 TraesCS6D01G157800 chr5B 77.041 196 38 6 3865 4056 520201125 520201317 5.580000e-19 106.0
52 TraesCS6D01G157800 chr5A 86.842 76 10 0 3138 3213 708410775 708410850 7.260000e-13 86.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G157800 chr6D 134334510 134338588 4078 True 7533.00 7533 100.000000 1 4079 1 chr6D.!!$R2 4078
1 TraesCS6D01G157800 chr6D 134739458 134743713 4255 True 3487.00 6002 97.080000 1 4079 2 chr6D.!!$R6 4078
2 TraesCS6D01G157800 chr6D 134586357 134588309 1952 True 2501.00 2501 89.898000 1092 3040 1 chr6D.!!$R3 1948
3 TraesCS6D01G157800 chr6D 135039807 135041759 1952 True 2490.00 2490 89.792000 1092 3040 1 chr6D.!!$R4 1948
4 TraesCS6D01G157800 chr6B 233672052 233674004 1952 True 2429.00 2429 89.228000 1092 3040 1 chr6B.!!$R2 1948
5 TraesCS6D01G157800 chr6B 233085574 233090873 5299 True 1332.00 3670 95.752667 716 3719 3 chr6B.!!$R3 3003
6 TraesCS6D01G157800 chr6A 176292007 176293959 1952 True 2479.00 2479 89.690000 1092 3040 1 chr6A.!!$R2 1948
7 TraesCS6D01G157800 chr6A 176002801 176003389 588 True 907.00 907 94.314000 649 1246 1 chr6A.!!$R1 597
8 TraesCS6D01G157800 chr6A 175992160 175997372 5212 True 803.45 2632 93.479750 1241 4079 4 chr6A.!!$R3 2838
9 TraesCS6D01G157800 chr3D 549233909 549234520 611 False 929.00 929 94.118000 1 611 1 chr3D.!!$F3 610
10 TraesCS6D01G157800 chr3D 157181942 157182553 611 False 896.00 896 93.137000 1 611 1 chr3D.!!$F1 610
11 TraesCS6D01G157800 chr3D 511421888 511422501 613 True 893.00 893 92.997000 1 611 1 chr3D.!!$R2 610
12 TraesCS6D01G157800 chr4D 360461333 360461947 614 True 924.00 924 93.821000 1 614 1 chr4D.!!$R1 613
13 TraesCS6D01G157800 chr2D 391826799 391827413 614 True 920.00 920 93.669000 1 615 1 chr2D.!!$R2 614
14 TraesCS6D01G157800 chr2D 200802199 200802809 610 False 907.00 907 93.475000 1 611 1 chr2D.!!$F1 610
15 TraesCS6D01G157800 chr2D 203458789 203459406 617 True 887.00 887 92.581000 1 619 1 chr2D.!!$R1 618
16 TraesCS6D01G157800 chr2D 565090943 565091845 902 False 340.00 340 74.123000 2094 2974 1 chr2D.!!$F5 880
17 TraesCS6D01G157800 chr2D 565052904 565053561 657 False 311.00 311 75.794000 2094 2732 1 chr2D.!!$F4 638
18 TraesCS6D01G157800 chr7D 383276892 383277507 615 False 893.00 893 92.857000 1 615 1 chr7D.!!$F3 614
19 TraesCS6D01G157800 chr7D 30264403 30264995 592 False 220.00 220 74.020000 1101 1699 1 chr7D.!!$F2 598
20 TraesCS6D01G157800 chr2A 705532001 705532655 654 False 337.00 337 76.444000 2094 2732 1 chr2A.!!$F1 638
21 TraesCS6D01G157800 chr2B 676747731 676748391 660 False 315.00 315 75.831000 2094 2732 1 chr2B.!!$F1 638
22 TraesCS6D01G157800 chr4A 698170390 698171061 671 True 248.00 248 74.138000 1091 1767 1 chr4A.!!$R1 676

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
687 899 0.106708 TATCCGGCATGTCTTCCAGC 59.893 55.0 0.00 0.0 0.00 4.85 F
1442 3244 0.595310 GCGGCGAGACCTACTTCATC 60.595 60.0 12.98 0.0 35.61 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 3726 1.366111 CCGGCGGACACATAACAAGG 61.366 60.0 24.41 0.0 0.0 3.61 R
3415 9063 0.108615 ATGTCGGCTCAGTCTTTCGG 60.109 55.0 0.00 0.0 0.0 4.30 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
240 241 2.526110 GGTTTGGGACTGGGGCTT 59.474 61.111 0.00 0.00 0.00 4.35
319 321 3.329814 ACGGTTCCCATTTAAGAAGGACT 59.670 43.478 0.00 0.00 0.00 3.85
568 572 4.153411 TCGTTTGTCCATTTTACCCCAAT 58.847 39.130 0.00 0.00 0.00 3.16
597 809 2.857744 CGGACAGGATAGGGTCGCC 61.858 68.421 0.00 0.00 34.87 5.54
676 888 1.142965 CACGTGATGGTATCCGGCA 59.857 57.895 10.90 0.00 0.00 5.69
681 893 1.070758 GTGATGGTATCCGGCATGTCT 59.929 52.381 0.00 0.00 0.00 3.41
682 894 1.768275 TGATGGTATCCGGCATGTCTT 59.232 47.619 0.00 0.00 0.00 3.01
683 895 2.224281 TGATGGTATCCGGCATGTCTTC 60.224 50.000 0.00 0.00 0.00 2.87
684 896 0.468226 TGGTATCCGGCATGTCTTCC 59.532 55.000 0.00 0.00 0.00 3.46
685 897 0.468226 GGTATCCGGCATGTCTTCCA 59.532 55.000 0.00 0.00 0.00 3.53
686 898 1.541233 GGTATCCGGCATGTCTTCCAG 60.541 57.143 0.00 0.00 0.00 3.86
687 899 0.106708 TATCCGGCATGTCTTCCAGC 59.893 55.000 0.00 0.00 0.00 4.85
719 931 2.365068 CGTCGACCAACGCTCTGTG 61.365 63.158 10.58 0.00 42.26 3.66
904 2700 3.677648 CTGCAGCAACCACCCAGC 61.678 66.667 0.00 0.00 0.00 4.85
992 2788 2.519063 CCAGCCACAGTGCCACAA 60.519 61.111 0.00 0.00 0.00 3.33
1130 2926 4.444838 TACGAGGCCAACGCGCAT 62.445 61.111 19.42 0.00 46.87 4.73
1438 3240 3.823330 CCGCGGCGAGACCTACTT 61.823 66.667 25.92 0.00 35.61 2.24
1439 3241 2.278013 CGCGGCGAGACCTACTTC 60.278 66.667 19.16 0.00 35.61 3.01
1440 3242 2.882876 GCGGCGAGACCTACTTCA 59.117 61.111 12.98 0.00 35.61 3.02
1441 3243 1.437986 GCGGCGAGACCTACTTCAT 59.562 57.895 12.98 0.00 35.61 2.57
1442 3244 0.595310 GCGGCGAGACCTACTTCATC 60.595 60.000 12.98 0.00 35.61 2.92
1443 3245 0.738975 CGGCGAGACCTACTTCATCA 59.261 55.000 0.00 0.00 35.61 3.07
3106 6020 6.401153 CGAGAGTTAAGAACCAAATGTACAGC 60.401 42.308 0.33 0.00 0.00 4.40
3158 6072 7.531857 TGCTCTGTCCCAAAATATAAAAACA 57.468 32.000 0.00 0.00 0.00 2.83
3349 8997 7.661127 TTTAATACAGTACAGACGCAATTGT 57.339 32.000 7.40 0.00 0.00 2.71
3367 9015 7.373180 CGCAATTGTTCATATACACACATACAC 59.627 37.037 7.40 0.00 0.00 2.90
3372 9020 7.039270 TGTTCATATACACACATACACTCACC 58.961 38.462 0.00 0.00 0.00 4.02
3386 9034 1.747355 ACTCACCCCTATGAACGTACG 59.253 52.381 15.01 15.01 0.00 3.67
3401 9049 0.804989 GTACGTACGCACACCCTACT 59.195 55.000 16.72 0.00 0.00 2.57
3412 9060 2.968574 CACACCCTACTCCTATGAGCAT 59.031 50.000 0.00 0.00 42.74 3.79
3415 9063 3.509575 CACCCTACTCCTATGAGCATCTC 59.490 52.174 0.00 0.00 42.74 2.75
3595 9243 2.509964 GTCCCTCTAACCATCCAACCAT 59.490 50.000 0.00 0.00 0.00 3.55
3880 9573 1.152963 GATGGCGGTAGGGTTGCAT 60.153 57.895 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 174 3.302129 GCCATGGGCCTTTGGAAG 58.698 61.111 24.65 4.4 44.06 3.46
266 267 2.842462 TCCACACTGTCCCACGCT 60.842 61.111 0.00 0.0 0.00 5.07
556 560 1.409101 CCCGTCCGATTGGGGTAAAAT 60.409 52.381 0.00 0.0 42.05 1.82
597 809 1.740296 CTAACGCCAACTCCACCGG 60.740 63.158 0.00 0.0 0.00 5.28
676 888 0.610232 GGGCAACTGCTGGAAGACAT 60.610 55.000 1.06 0.0 41.70 3.06
904 2700 1.466558 GGCTCTGCTTTCTTCTTTCCG 59.533 52.381 0.00 0.0 0.00 4.30
1438 3240 3.196939 TGTTGGCGATGATGATGATGA 57.803 42.857 0.00 0.0 0.00 2.92
1439 3241 3.065648 TGTTGTTGGCGATGATGATGATG 59.934 43.478 0.00 0.0 0.00 3.07
1440 3242 3.065786 GTGTTGTTGGCGATGATGATGAT 59.934 43.478 0.00 0.0 0.00 2.45
1441 3243 2.419673 GTGTTGTTGGCGATGATGATGA 59.580 45.455 0.00 0.0 0.00 2.92
1442 3244 2.478370 GGTGTTGTTGGCGATGATGATG 60.478 50.000 0.00 0.0 0.00 3.07
1443 3245 1.745087 GGTGTTGTTGGCGATGATGAT 59.255 47.619 0.00 0.0 0.00 2.45
1915 3726 1.366111 CCGGCGGACACATAACAAGG 61.366 60.000 24.41 0.0 0.00 3.61
2483 4319 2.157738 GCTCTTGAGGTTCTTGTGCAT 58.842 47.619 0.00 0.0 0.00 3.96
3106 6020 1.000896 ACCGGATGGGGAAAAGCTG 60.001 57.895 9.46 0.0 41.60 4.24
3130 6044 6.757897 TTATATTTTGGGACAGAGCAAGTG 57.242 37.500 0.00 0.0 42.39 3.16
3207 6121 6.655078 TCTTTTAGCTGATTTTTGCTCCTT 57.345 33.333 0.00 0.0 40.35 3.36
3346 8994 7.547722 GGTGAGTGTATGTGTGTATATGAACAA 59.452 37.037 0.00 0.0 0.00 2.83
3347 8995 7.039270 GGTGAGTGTATGTGTGTATATGAACA 58.961 38.462 0.00 0.0 0.00 3.18
3349 8997 6.407639 GGGGTGAGTGTATGTGTGTATATGAA 60.408 42.308 0.00 0.0 0.00 2.57
3367 9015 1.747355 ACGTACGTTCATAGGGGTGAG 59.253 52.381 16.72 0.0 0.00 3.51
3386 9034 1.755179 TAGGAGTAGGGTGTGCGTAC 58.245 55.000 0.00 0.0 0.00 3.67
3401 9049 3.319405 GTCTTTCGGAGATGCTCATAGGA 59.681 47.826 0.00 0.0 36.61 2.94
3412 9060 0.608308 TCGGCTCAGTCTTTCGGAGA 60.608 55.000 0.00 0.0 40.01 3.71
3415 9063 0.108615 ATGTCGGCTCAGTCTTTCGG 60.109 55.000 0.00 0.0 0.00 4.30
3595 9243 7.177216 ACTGATTTGAAATTGCAGACCAATCTA 59.823 33.333 11.99 0.0 43.22 1.98
3901 9595 7.009815 GCGTACAAGCACTGTATTTGATACTTA 59.990 37.037 9.55 0.0 42.50 2.24


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.